Biology for Computer Engineers:Part 1()

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Biology

For Computer EngineersPart 1: Chemistry for Biology

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Biological studies need computingAdvanced imagingDatabase technologiesData miningGraphical modeling

DNA/Protein modeling

Analysis softwareAdvanced computing needs biological models

Semantic systemsMachine learningRobotics

Why me, the computer geek?


Study of lifeLiving things are all around us

They are like complex software systemsEasy to see design patterns

CompositionAggregationEvents and signals…and so on

OOAD beginnings were based on biological models

What is Biology?


Top-downStudy of living beings leads to study of cells and molecules

historic evolution of biologyBottom-up

Study of how molecules and cells combine to form living beings

Trend today – molecular biologyWe follow the latter

Approaches to Biology


CompositionAll living beings are composed of cellsCells are composed of moleculesMolecules are composed of atoms, and so on…

Interactions between composed systems are predictable

Individual outcomes are deterministic and repeatableHigher order biological systems are very complex

increased complexity reduces predictabilityAdvances in science would bring more predicabilityThere is a role for heuristics

Composition in Biology


All living beings are classified in a hierarchical treeTaxonomy

Cells are of different typesEach type of tissue is made of a different type of cell

Nerve cells, different types of heart cells Different types of complex molecules

Carbohydrates, proteins, fats There are inheritance trees everywhere

Inheritance and Classification


All biology starts from chemical reactionsbetween organic molecules

that create organic molecules What are organic molecules?

Molecules containing Carbon (C)

Combinations of C with H, O, N

Other elements present in small quantities

Sulphur, Phosphorous, Iron, Sodium etc.

These elements form organic building blocks using covalent bonds

Hydroxyl – OH-

Acid - COOH

Amine – NH2+, and so on…

Organic Chemistry for Biology


Organic building blocks form chainsBonds between building blocks

Long or short chains, three dimensional growth

Multi-branched, looks like a many-headed hydra

Growth controlled by weak molecular forces

Electrostatic attraction between groups with opposite charge

Hydrogen bonds

Attraction between an O or N atom in a molecule with an H atom in another molecule

Van der Waal’s bonds, hydrophobic bonds etc.

Environmental factors can control growth of organic molecules

In solution, Temperature, Pressure, Electric fields etc.

These factors can overcome weak forces

Organic Molecules


Structure of Organic Molecules

Formaldehyde Cholesterol

COH


All organic molecules are not bio-moleculesPetrol is an organic molecule, but it has no role in biology

Bio-molecules are those that participate in the process of life

Fats (lipids)CarbohydratesAmino Acids, ProteinsNucleic Acid (DNA, RNA)…

Now, we are at the gates of molecular biology

Bio-Molecules


Two organic building blocks at endsAn Amine (NH2+)

An Acid (COOH-)

Can string together easily to form chains

Peptide link

NH2+ on one amino acid binds with COOH- on another

Generally stable, breaks slowly in the presence of water

Peptides can chain together to form polypeptides

Polypeptides chain to form Proteins

Amino acids are monomers, (poly)peptides are polymers

Monomers have a single molecular structure

Polymers are made of repeated monomers

Amino Acids


Amino Acids

Glucagon(polypeptide hormone)

Glycine – simplest amino acid(NH2-CH2-COOH)


Proteins are the most important bio-moleculesArguably – perhaps, DNA and RNA are the most important

Complex, very large organic molecules

Formed from 20 different amino acids Multiple functions that are important for cells

Assistance to metabolism – enzymes etc.

Maintaining cell shape

Inter-cell and intra-cell signalling – hormones etc.

Parts of proteins formed by certain types of peptide chains provide these functions

Called Domains

No other bio-molecule has this versatility

Proteins


Polypeptides are amino acid chainsThese chains can fold in 3 dimensions

They have only one strand Proteins have secondary structure

Lateral attraction between multiple polypeptide strands forming sheets or helices

These strands might be different parts of the same chain Proteins have tertiary structure

Sequence of sheets and helices fold in 3 dimensions

Depends on attractive forces between different parts of the sequence

Proteins can have quaternary structureMultiple polypeptide chains with tertiary structure develop attractions and align in a formation

Not all proteins have quaternary structure

Structure of Proteins


Primary StructureEach bead in the chain is an amino acid.

Amino Acids are represented by 3-letter abbreviations. Upto 20 amino acids are used to make proteins.

Each Amino Acid has unique chemical properties:

Hydrophobic/hydrophilicAcidic/Basic, etc.

Some Amino Acids can be manufactured by the body. Amino Acids that are not manufactured have to be taken through food. These are Essential Amino Acids.


Secondary Structure

Sheet formation

Helix formation

Each strand in a sheet is represented by a pointed ribbon


Tertiary StructureA protein secondary structure might be a sequence of sheets and helices.

The secondary structure folds in 3-d space due to attractive forces. This creates the tertiary structure.


Quaternary StructureCollagen triple helix: There are three polypeptide chains intertwined with each other to form the thread-like collagen structure. Collagen is used to make long muscular tissue like ligaments

Haemoglobin consists of 4 polypeptide chains, each containing a heme group (that contains iron, shown in green)


Importance of Protein StructureImpact of Primary Structure modification: the curious case of Sickle Cell Anaemia

Amino-acid in position 6 of one of the haemoglobin sub-units is different in people with Sickle Cell Anaemia.

Haemoglobin molecules float around in red blood cells (RBCs). Oxygen binds to them in lungs and unbinds in tissues. This is how tissues receive Oxygen.

In de-oxygenated state, modified haemoglobin molecules stick together to form long chain polymers which then bundle together like a rigid multi-strand braid.

The braid causes affected RBCs to bend like a sickle. They become normal again upon oxygenation.

Repeated change in structure causes rupture and destruction of RBCs

de-oxy

oxy

de-oxygenatedstate


Importance of Protein Structure Protein denaturing,

misfolding, aggregationLoss of secondary, tertiary, quaternary structures

Does not affect primary structure

Caused by Heat, Chemical /Biological agents, Pressure

Reversible in some cases

Examples

Egg white becomes white when boiled

Skin on curdled milk

Denatured protein molecules sometimes stick together

Forms aggregates

Loss of structure and disease

Loss of structure renders proteins dysfunctional

Functions that depend on the protein are affected

Aggregates might be toxic or might interrupt activity of cells

Examples

Alzheimer’s disease

Parkinson’s disease

Mad Cow disease

This is a major research area


We open the door to molecular biology, and meet…

The Cell

In Part 2…


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Biology for Computer Engineers:Part 1()